X-RAY STUDIES ON THE STRUCTURE OF DES-PENTAPEPTIDE INSULIN AT 2.4 RESOLUTION——THE DPI MOLECULE AND ITS STRUCTURAL RELATIONSHIP WITH INSULIN

The structure of the monomeric insulin analogue des(B26—B30) insulin is presented.; A detailed comparison with the 2Zn insulin structures shows that while there are some large changes in the structure, the basic secondary structural units maintain their integrity. The DPI structure is broadly similar to molecule Ⅰ in the 2Zn structure, and in this respect is like other crystal forms of insulin. In addition to changes on the surface of the structure there are some subtle but extensive changes in the heart of the molecule. The molecules are closely packed in the crystal with many and varied contacts, including a complex network of protein-cadmium interactions and a considerable number of water mediated contacts. The molecular surface has an unusually large number of hydrophobic groups which tend to cluster in a thick band running around the protein. The crystal structure is well ordered, indeed the clarity of some side chains and the definition of the water molecules is superior to that found in the mor     

Theoretical studies on the influence of molecular interactions on the mechanism of electron transfer in photosynthetic reaction center of Rps.viridis

Based on the QM/MM optimized X-ray crystal structure of the photosynthetic reaction center (PRC) of purple bacteria Rhodopseudomonas (Rps.) viridis, quantum chemistry density functional method (DFT, B3LYP/6-31G) has been performed to study the interactions between the pigment molecules and either the surrounded amino acid residues or water molecules that are either axially coordinated or hydrogen bonded with the pigment molecules, leading to an explanation of the mechanism of the primary electron-transfer (ET) reactions in the PRC. Results show that the axial coordination of amino acid residues greatly raises the ELUMO of pigment molecules and it is important for the possibility of ET to take place. Different hydrogen bonds between amino acid residues, water molecules and pigment molecules decrease the ELUMO of the pigment molecules to different extents. It is crucial for the ET taking place from excited P along L branch and sustains that the ET is a one-step reaction without through accessory bacterioc     

Properties of a water layer on hydrophilic and hydrophobic self-assembled monolayer surfaces: A molecular dynamics study

The microscopic behaviors of a water layer on different hydrophilic and hydrophobic surfaces of well ordered self-assembled monolayers (SAMs) are studied by molecular dynamics simulations. The SAMs consist of 18-carbon alkyl chains bound to a silicon(111) substrate, and the characteristic of its surface is tuned from hydrophobic to hydrophilic by using different terminal functional groups ( CH 3 , COOH). In the simulation, the properties of water membranes adjacent to the surfaces of SAMs were reported by comparing pure water in mobility, structure, and orientational ordering of water molecules. The results suggest that the mobility of water molecules adjacent to hydrophilic surface becomes weaker and the molecules have a better ordering. The distribution of hydrogen bonds indicates that the number of water-water hydrogen bonds per water molecule tends to be lower. However, the mobility of water molecules and distribution of hydrogen bonds of a water membrane in hydropho- bic system are nearly the same as those in pure water system. In addition, hydrogen bonds are mainly formed between the hydroxyl of the COOH group and water molecules in a hydrophilic system, which is helpful in understanding the structure of interfacial water.     

Structures of N—（2,3,4,6—Tetra—O—acetyl—β—D—glycosyl） thiocarbamic Benzoyl Hydrazine

The crystal structure of N-(2,3,4,6-tetra-O-acetyl-β-D-gly-cosyl)-thiocarbamic benzoyl hydrazine(C22H27N3O9S) was determined by X-ray diffracton method.The hexopyranosyl ring adopts a chair conformation.All the ring substituents are in the equatorial positions.The acetoxyl-methyl group is in synclinal conformation.The S atom is in synperiplanar conformation while the benzoyl hydrazine moiety is anti-periplanar.The thiocarbamic moiety is almost companar with the benzoyl hydrazine group.There are two intramolecular hydrogen bonds and one intermolecular hydrogen bond for each molecule in the crystal structure.The molecules form a network structure through intermolecular hydrogen bonds.     

苯四甲酸桥连的镍配合物[Ni(btec)(H2O)4][Ni(imi)2(H2O)4]·2H2O的合成及结构

At room temperature, a coordination polymer [Ni(btec)(H2O)4][Ni(imi)2(H2O)4]·2H2O was synthesized by reaction of NiCl2·6H2O, 1,2,4,5-benzenetetracarboxylic dianhydridc and imidazole in a water/THF solution. The structure was determined by X-ray diffraction crystal structure analysis. It crystallizes in triclinic P1 space group with the crystal cell parameters of a=0.67542 (2) nm, b=1.000 14 (1) nm, c=1.09088 (3) nm, α=74.140(2)°, β= 74.388(1)°, y=73.239(2)°, and V=0.664 09(3) nm3, Z=1. The crystal structure shows that Ni1 atom is coordinated by four water and two imidazole molecules, while Ni2 is coordinated by four water molecules and two carboxyl oxygen atoms. The 1,2,4,5-benzenetetracarboxylate ions bridge Ni2 coordination centers to form one-dimensional chain structure. Moreover, the chains are further linked together by hydrogen bonds to form a two-dimensional network. CCDC: 295873.     

Spectroscopic Studies of a Three-dimensional,Five-coordinated Copper(Ⅱ） Complex via Hydrogen Bonds:[Cu(PPD)(H2O)2](H2PDA=Pyridine-2,6-dicarboxylic Acid)

A new copper(Ⅱ） complex[Cu(PDA)(H2O)2] was synthesized and its structure was determined.Cu(Ⅱ）is five-coordinated in a tetragonal pyramid geometry.The two coordinating water molecules are different and the two Cu-O bond lengths differ by nearly 0.02nm.The whole crystal is linked to form a three-dimensional network by means of hydrogen bonds.The X-band ESR spectrum shows three different g tensors with a well-resolved hyperfine structure in the gz signal,giving the ESR parameters gx=2.05,gy=2.065 and gz=2.29.The covalency of the coordinate bonds and the deviation from tetragonal pyramid geometry for the complex are discussed based on the ESR spectra.     

REFINED CRYSTAL STRUCTURE OF INSULIN AT 1.8A RESOLUTION——HYDROGEN BONDS AND BOUND WATER

The hydrogen bonds in insulin fall into three cases: the helical hydrogen bonds in α- or 3_(10)helices, the non-helical one formed by polar groups of insulin itself, and the hydrogen bondsformed between insulin and water. By using the information obtained, the results of a seriesof biochemical investigations on insulin analogs related to B-chain C-terminal peptide can beinterpreted and it can also be inferred that the complex behaviours of the aggregation ofinsulin may play a protective role for the unique conformation of the molecule. Water structure also appears in the refined model. About one third of the water in anasymmetric unit is hydrogen-bonded to insulin molecules or each other, which are referred toas bound water. The polar and charged groups of insulin all show the tendencies to bind towater molecules as many as possible, which is a significant factor for the stabilization of theunique conformation of the molecule. The binding way of water molecules to insulin mole-cules is also analysed.     

Evolution of Conformation and Dynamics of Solvents in Hydration Shell along the Urea-induced Unfolding of Ubiquitin

A clear diagram for the unfolding of protein induced by denaturant is a classical but still unsolved challenge. To explore the unfolded conformations of ubiquitin under different urea concentrations, we performed hybrid Monte Carlo-molecular dynamics simulations (MC-MD) guided by small angle X-ray scattering (SAXS) structural information. Conformational ensembles sampled by the hybrid MC-MD algorithm exhibited typical 3D structures at different urea concentrations. These typical structures suggested that ubiquitin was subjected to a sequential unfolding, where the native contacts between adjacent β-sheets at first were disrupted together with the exposure of hydrophobic core, followed by the conversion of remaining β-strands and helices into random coils. Ubiquitin in 8 mol·L?1 urea is almost a random coil. With the disruption of native structure, urea molecules are enriched at protein hydrated layer to stabilize newly exposed residues. Compared with water, urea molecules prefer to form hydrogen bonds with the backbone of ubiquitin, thus occupying nodes of the hydrogen bonding network that construct the secondary structure of proteins. Meanwhile, we also found that the slow dynamics of urea molecules was almost unchanged while the dynamics of water was accelerated in the hydration shell when more residues were unfolded and exposed. The former was also responsible for the stabilization of unfolded structures.     

Molecular dynamics simulations of the hydration of poly(vinyl methyl ether):Hydrogen bonds and quasi-hydrogen bonds

Atomistic detailed hydration structures of poly(vinyl methyl ether)(PVME) have been investigated by molecular dynamics simulations under 300 K at various concentrations. Both radial distribution functions and the distance distributions between donors and acceptors in hydrogen bonds show that the hydrogen bonds between the polymer and water are shorter by 0.005 nm than those between water molecules. The Quasi-hydrogen bonds take only 7.2% of the van der Waals interaction pairs. It was found the hydrogen bonds are not evenly distributed along the polymer chain,and there still exists a significant amount(10%) of ether oxygen atoms that are not hydrogen bonded to water at a concentration as low as 3.3%. This shows that in polymer solutions close contacts occur not only between polymer chains but also between chain segments within the polymer,which leads to inefficient contacts between ether oxygen atoms and water molecules. Variation of the quasi-hydrogen bonds with the concentration is similar to that of hydrogen bonds,but the ratio of the repeat units forming quasi-hydrogen bonds to those forming hydrogen bonds approaches 0.2. A transition was found in the demixing enthalpy at around 30% measured by dynamic testing differential scanning calorimetry(DTDSC) for aqueous solutions of a mono-dispersed low molecular weight PVME,which can be related to the transition of the fractions of hydrogen bonds and quasi-hydrogen bonds at ～27%. The transition of the fractions of hydrogen bonds and quasi-hydrogen bonds at ～27% can be used to explain the demixing enthalpy transition at 30% at a molecular scale. In addition,at the concentration of 86%,each ether oxygen atom bonded with water is assigned 1.56 water molecules on average,and 'free' water molecules emerge at the concentration of around 54%.     

CRYSTAL AND MOLECULAR STRUCTURE OF DEHYDROCRYDALINE CHLORIDE

The crystals of alkaloid Dehydrocrydaline chloride (C_(22)H_(24)NO_4·HCl) belong to the orthorhombic system. The space group is D_(2k)~(14)-Pbcn with the unit cell parameters of a=8.528,b=23.317 and c=24.798, and eight molecules per unit cell. The coordinates for all the non-hydrogen atoms were found by using direct methods and Fourier syntheses. During the course of refinement of this structure (using least squares and difference Fouriers), it was discovered that there are 4.5 water molecules with different occupancies in one asymmetric volume of the unit cell. The anisotropic refinement of non-hydrogen atoms and the isotropic refinement of non-aqueous hydrogen atoms led to a final R-factor of 0.053. Water molecules formed a relatively complex network around chloride ion.In this paper the small molecule structure and the network of water molecules are described.     

Hydrogen Bonding Assembled 3D Supramolecular Structures Formed by 5-Amino-2,4,6-triiodoisophthalic Acid and N-Heterocyclic Aromatic Ligands

Three salts constructed by 5-amino-2,4,6-triiodoisophthalic acid(ATIPA) with N-heterocycles aromatic coformers such as pyridine tetrazolium, tetramethylpyraziiie and cyanuric acid were synthesized by slowing evaporation of solvent. X-Ray single crystal analysis shows that hydrogen protons of the carboxyl groups transfer to nitrogen atoms of the N-heterocyclic coformers to form N-H…0 hydrogen bonds in all the three compounds. A huge amount of H-bonds play significant role in tlie construction of these compounds and all of them generate 3D structures through strong O-H…N, O-H…O, N-H…O and weak C-H…O hydrogen bonds. Moreover, solvent water molecules are indispensable in the formation of compounds 1 and 3, which constitutes different supramolecular synthons to bridge individual molecules and chains to form stable structures. In addition, these crystal structures were further characterized by themiogravimetric analysis and infrared spectroscopy.     

Cytosinium Isophthalate: Crystal Structure Redetermination and Room Temperature Phosphorescence

The title compound cytosinium isophthalate(C-H_2IA) self-assembly of cytosine(C) and isophthalic acid(H_2IA) in aqueous media has been synthesized and the crystal structure with a reasonable protonation state is redetermined. Single-crystal X-ray diffraction analysis reveals that each asymmetric unit contains one protoned cytosine molecule and one deprotoned isophthalic acid. The proton transferred from carboxylic acid to the pyrimidine ring is disordered across an inversion center with occupancy of 0.5 and the proton located to one of the carboxylate group lies on an inversion center shared by two crystallographically equivalent oxygen atoms. In addition, the cytosine molecules are connected by complementary hydrogen bonds to form a one-dimensional tape structure. The neighboring isophthalic acids are connected via hydrogen bonds between carboxyl groups to form a one-dimensional lattice like tape. Furthermore, the adjacent organic base tapes and organic acid tapes are stacked one with another through π-π stacking interactions to form a three-dimensional supramolecular structure. Interestingly, C-H_2IA displays a green phosphorescence in solid state at room temperature with the lifetime of 0.7 s determined by time resolved studies, indicating that supramolecular C-H_2IA is a potential pure organic phosphorescent luminogens.     

DFT Study on the Effect of Hydrogen-bond Formation on the Adsorption of Aminotriazines on Graphene

DFT calculations have been performed to explore the aminotriazine adsorption on graphene surfaces.Relative energies,equilibrium geometries and electronic structures of monomer and dimer of aminotriazine molecules adsorbed at the surface were investigated and analyzed in details.It was found that the hydrogen atoms in the NH2 group of aminotriazine molecules are directed toward the graphene surface,and the adsorption energy increases as the NH2 group is added.The adsorbed aminotriazine molecules facilely form a dimer through the hydrogen bonding interactions,and the two aromatic rings of optimized structure of 2-amino-1,3,5-triazine(B) dimmer(denoted by B2) and melamine(D) dimmer(denoted by D2) are parallel to the graphene sheet.The large deviation of the averaged adsorption energy of B2 and D2 compared to monor adsorption may reflect the increase of π-π repulsion and the effect of hydrogen bond formation.The electronic structure analyses reveal that the formation of hydrogen bonds in melamine dimer has great influence on the adsorption mode at the graphene surface.     

Hydrogen bonding interactions between ethylene glycol and water: density,excess molar volume,and spectral study

Studies of the density and the excess molar volume of ethylene glycol (EG)-water mixtures were carried out to illustrate the hydrogen bonding interactions of EG with water at different temperatures. The re-sults suggest that a likely complex of 3 ethylene glycol molecules bonding with 4 water molecules in an ethylene glycol-water mixture (EGW) is formed at the maximal excess molar volume,which displays stronger absorption capabilities for SO2 when the concentration of SO2 reaches 400×10?6 (volume ratio) in the gas phase. Meanwhile,FTIR and UV spectra of EGWs were recorded at various EG concentra-tions to display the hydrogen bonding interactions of EG with water. The FTIR spectra show that the stretching vibrational band of hydroxyl in the EGWs shifts to a lower frequency and the bending vibra-tional band of water shifts to a higher frequency with increasing the EG concentration,respectively. Furthermore,the UV spectra show that the electron transferring band of the hydroxyl oxygen in EG shows red shift with increasing the EG concentration. The frequency shifts in FTIR spectra and the shifts of absorption bands in UV absorption spectra of EGWs are interpreted as the strong hydrogen bonding interactions of the hydrogen atoms in water with the hydroxyl oxygen atoms of EG.     

The Important Roles of Water in Protein Folding: an Approach by Single Molecule Force Spectroscopy

The single-chain elasticity of a completely unfolded protein ((I27)8,modules of human cardiac titin) is studied in different liquid environments by the atomic force microscopy (AFM)-based single molecule force spectroscopy (SMFS).The experimental results show that there is a clear deviation between the force curves obtained in the aqueous and nonaqueous environments.Such a deviation can be attributed to the additional energy consumed by the rearrangement of the bound water molecules around the chain of the completely unfolded (I27)8 chain upon stretching in aqueous solution,which is very similar to the partial dehydration process from a denatured/unfolded to a native/folded protein.Through the analysis of the free energy changes involved in protein folding,we conclude that it is due to the weak disturbance of water molecules and the special backbone structures of proteins that the self-assembly of proteins can be achieved in physiological conditions.We speculate that water is likely to be an important criterion for the selection of self-assembling macromolecules in the prebiotic chemical evolution.     

Synthesis and Crystal Structure of 1-H-Pyrrole-2-carboxylic Acid [2-(Naphthalen-1-ylamino)-ethyl]-amide

1 INTRODUCTION Pyrrole based compounds are frequently observed as hosts for neutral molecules[1] and anionic spe- cies[2]. Meantime, it is found that these compounds also have the ability to form higher order self-assem- bled ensembles and aggregates in solid state through hydrogen bonds[3]. In previous work, we have re- ported the crystal structures of two pseudopoly- morphs of o-di-(pyrrole-2-carboxamides)-phenylene 1[4]. A helical assembly is observed when 1 forms specific hydrogen bon…     

Conformation of 1,2-Dimethoxyethane in Water

To understand the conformation of 1,2-dimethoxyethane (DME) in water, a system of two kinds of molecules, DME and H_2O, was focused. The interaction of various conformers of DME with water was studied by means of ab initio molecular orbital calculation with 6-31G (d) basis set. It is shown that there are two forms of interactions between the two molecules in the system, the close touched (H_2O attaches to the two oxygen atoms of DME) and the open touched (H_2O attaches to one oxygen atom of DME) structures. The conformation of DME is remarkably influenced by the interactions. Instead the ttt conformer is preferred in the gas state, with a close touched H_2O the tgt conformer becomes the most stable one. The obtained hydration energies show that the stabilized order of DME conformers by water is tgt>tgg′>ttt.     

AN INVESTIGATION ON THE ab initio CALCULATION OF INTERMOLECULAR INTERACTION——NON-BONDED INTERACTION IN THE HYDROGEN BOND COMPLEX (HF)_2

An ab initio calculation of the hydrogen bond complex (HF)_2 is given with the 6-311 G~(**) basis set, according to which the potential surface around the balance point of the distancès and the orientations between two HF molecules is obtained. The atomic charges in the system are calculated with the PD/LSF method (potential-derived/least-square-fitting method) and then an analysis of the hydrogen bond interaction between two HF molecules is given with the (exp-6-1) potential function, by means of which it is shown that the main interaction between them is not an electro-static but a charge transfer one. The potential curve between two HF molecules is like a Morse function.     

Influence of temperature on the structure of liquid water

Molecular dynamics simulations have been carried out for liquid water at 7 different temperatures to understand the nature of hydrogen bonding at molecular level through the investigation of the effects of temperature on the geometry of water molecules. The changes in bond length and bond angle of water molecules from gaseous state to liquid state have been observed, and the change in the bond angle of water molecules in liquid against temperature has been revealed, which has not been seen in literature so far. The analysis of the radial distribution functions and the coordinate numbers shows that, on an average, each water molecule in liquid acts as both receptor and donor, and forms at least two hydrogen bonds with its neigbors. The analysis of the results also indicates that the water molecules form clusters in liquid.     

Synthesis and Structure of Manganese Coordinated Polymer with Regular X-shaped Cavity

A coordination polymer [Mn(IDA)2(H2o)47, (H2IDA=N-iminodiacetic acid) was synthesized and char-acterized by single crystal X-ray diffraction. The crystal belongs to the tetragonal system, the space group is P-421C with the crystal cell parameters a=0.81120(8) nm, b=0.81120(8)nm, c=0.96196(4)nm, V=0.6330(1)nm^3, Mr=355.17, R=0.0224, ωR=0.061. The four carboxylic oxygen atoms of the differentN-iminodiacetic acid ligands and two water molecules coordinate to the manganese atom. The manganeseatom is in an approximates octahedral coordination sphere. Each carboxylic acid ligand bridges two man-ganese atoms, forming two zig-zag supramolecular chains. The twisted chains construct a two-dimension lay-er structure with regularly arranged X-shaped window cavity. The three-dimension supramolecular networkis formed by coordination bonds and hydrogen bonds.